Now out from Bintu lab: compaction following transient KRAB recruitment tracks long-term epigenetic memory. But K9me3 decays after KRAB release and is replaced by DNA methylation. Does compaction help maintain K9me3, or slow its loss enough to facilitate the handoff to DNAme? tinyurl.com/ycay4mrh

Single-cell chromatin state transitions during epigenetic memory formation

Large-scale chromatin compaction quantitatively predicts the percentage of cells with durable epigenetic memory of gene silencing.

tinyurl.com

@mileshuseyin.bsky.social and the lab have put together a comprehensive protocol for genome-wide Micro-C and for Region-Capture Micro-C in @natprot.nature.com : www.nature.com/articles/s41... See also the GitHub for a user-friendly end-to-end computational pipeline: github.com/ahansenlab/M...

Nature Protocols@natprot.nature.com · 3w ago

New Article! Mapping 3D genome organization at nucleosome-scale with Micro-C and Region Capture Micro-C (RCMC)

Out now in Science! Our study challenges long-standing assumptions about transcription factor specificity in eukaryotes. Novel single-molecule measurements of TF behavior in living cells reveal an independence of locus-specific binding from DNA sequence recognition.🧵 www.science.org/doi/10.1126/...

Unstructured transcription factor interactions enable emergent specificity

How intrinsically disordered regions (IDRs) shape chromatin binding and nuclear organization of transcription factors (TFs) remains unclear. We used proximity-assisted photoactivation (PAPA), a single...

science.org

Today, it was Lisa's turn to defend her PhD thesis and she did an absolutely fantastic job 😍 Especially going into full structure of the RNA Pol2 catalytic core and explaining the mutants. It was an outstanding discussion! I am really proud of her performance today 🥹

Very excited to share our newest findings! A very long team effort pursued by multiple team members -to frantically reproduce everything over and over-, we show mTOR-Polycomb synergy at promoters of developmental master regulator TFs in ESCs prior to their expression. www.biorxiv.org/content/10.6...

Excited to share our latest work in Molecular Cell: www.cell.com/molecular-ce... We show that PRC1 condensates exclude SWI/SNF from chromatin, revealing a physical mechanism for how opposing regulators compete to control gene expression. Huge thanks to all collaborators and mentors!

Mutual antagonism between PRC1 condensates and SWI/SNF in chromatin regulation

Niekamp et al. show that biomolecular condensates formed by Polycomb repressive complexes can physically restrict access of the activating remodeler SWI/SNF to chromatin. Establishing this barrier dep...

cell.com

Johannes Stein's new lab at the MPIMG will use microscopy to study the organization of the genome at a molecular level. We talked to him about how, despite being a trained physicist, he ended up in biology, the potential of his research and the power of interdisciplinary teams. @jmstein.bsky.social

A nanoscopic look at gene regulation

Johannes Stein joined the MPIMG in 2025. His lab will use state-of-the-art microscopy techniques to examine the organisation of the genome at a molecular level. We talked to him about how, despite bei...

molgen.mpg.de

The next iteration of O-MAP targeting genomic loci is now at eLife!! DNA O-MAP enables proximity labeling at specific DNA loci took a ton of work from many lab members and collaborators, so it's really exciting to wrap up this paper with @oligopain.bsky.social! elifesciences.org/articles/102...

DNA O-MAP uncovers the molecular neighborhoods associated with specific genomic loci

DNA O-MAP enables proximity labeling at specific genomic loci in fixed cells using programmable oligonucleotides, revealing locus-proximal proteomes and chromatin interactions without genetic modifica...

elifesciences.org

Delighted to share our preprint describing COMET, a new approach to drift correction for #SMLM, which performs exceptionally well in practice. Check out the benchmarking results compared to other methods! :) Thanks to @lreinkensmeier.bsky.social for a superb effort. www.biorxiv.org/cgi/content/...

Please check out our newest work on fluorogenic speed imager probes, in which we combine the strengths of speed-optimized imagers and fluorogenic imagers. #SuperResolution #DNAPAINT #microscopy www.biorxiv.org/content/10.6...

It’s incredibly hard to study lipids in biological membranes on the nanoscale. You need near-perfect information on both membrane ultrastructure and lipid density. Lipid-CLEM, now out in @natcellbio.nature.com brought to you by @mathilda95.bsky.social changes that: www.nature.com/articles/s41...

Our most recent work on the “function and evolution” of #nuclear-speckles is now online at Cell @cp-cell.bsky.social doi.org/10.1016/j.ce... Read the thread👇 for the highlights of our findings.

🚨 We’re happy to announce (finally!) the publication of METALoci, in collaboration with @dariloops.bsky.social and heroes: @jrotwitguez.bsky.social & @imotagom.bsky.social. METALoci integrates #3DGenome and #Epigenetics data into a unified framework we believe is very useful! Here 👉🏻 rdcu.be/e5sm2

Chromatin spatial analysis by METALoci unveils sex-determining 3D regulatory hubs

Nature Structural & Molecular Biology - METALoci, a new three-dimensional genome computational tool, reveals a major rewiring of regulatory interactions during sex determination. By combining...

rdcu.be

Get to know Thomas Schlichthärle, our newly appointed professor of #AI-guided #ProteinDesign, in the latest NewIn episode. He wants to use custom-designed #proteins to advance the development of new #medicines: go.tum.de/484027 #HightechAgendaBayern ▶️ youtu.be/G-pt28HJpA8 📹& 📷ProLehre

Designing proteins for targeted cell activation

Prof. Thomas Schlichthärle spricht über seine Arbeit als Professor für AI-guided Protein Design.

go.tum.de

We;re hiring Junior Group Leaders! 🔬✨ We’re looking for researchers in immunology, chemical biology, AI in biology, or protein design to launch their own independent groups in our collaborative, international environment. www.nki.nl/news-events/...

Please spread the word: the Structural Studies Division @mrclmb.bsky.social is looking for a new tenure-track, independent group leader with an exciting plan in any area of Structural (Molecular & Cell) biology, in discovery biology and/or methods development. 🥳 mrc.tal.net/vx/mobile-0/...

Rewrote my Python bioformats wrapper (from aicsimageio/bioio) as a standalone package: - fully bootstrapped Java setup (just pip install) - lazy, repeatably-indexable Array object - fully spec-compliant OME-Zarr group obj. - xarray/dask exports github.com/imaging-form... v0.0.rc1 on PyPI

GitHub - imaging-formats/bffile: Modern Bio-Formats wrapper with clean lazy Python API

Modern Bio-Formats wrapper with clean lazy Python API - imaging-formats/bffile

github.com

New paper alert!🤩Super proud that our story led by superstar postdocs @liujinghui.bsky.social and @nerlielisa.bsky.social is finally out! We found how electrical signals are key for promoting organ regenerative growth!!! A thread 🧵https://www.science.org/doi/10.1126/sciadv.aec0687

Injury-induced electrochemical coupling triggers organ growth

Organ repair and growth rely on coupling tissue-wide membrane depolarization with intracellular proliferative signaling.

science.org

I’m excited to share my first-author paper, with co-first author @rongqinxiaoxiao.bsky.social, now out in @nature.com. We developed a live-cell single-particle tracking platform to see how TRiC & prefoldin engage proteins during co- and post-translational folding. 1/9 www.nature.com/articles/s41...

Single-molecule dynamics of the TRiC chaperonin system in vivo - Nature

Single-particle tracking experiments in intact cells reveal dynamic co- and post-translational interactions of the TRiC–PFD chaperonin complex with client proteins during in vivo protein folding.

nature.com

Great to see our Science Review on emerging multiplexed single-molecule methods that use libraries to link sequence to dynamics. A fun collaborative writing project! From sequence to function: Bridging single-molecule kinetics and molecular diversity | Science www.science.org/doi/10.1126/...

From sequence to function: Bridging single-molecule kinetics and molecular diversity

Biological function is fundamentally determined by nucleic acid and protein sequence. Beyond encoding genetic information, nucleic acids also display complex physicochemical parameters that shape stru...

science.org

Formation & function of #MembranelessOrganelles! #CryoET structures of #proteasome storage granules inside cells! Read our paper @cp-cell.bsky.social! ❕Publication: doi.org/10.1016/j.ce... ❕Press Release: www.biochem.mpg.de/en/pressroom @uoftmedicine.bsky.social @erc.europa.eu #UPSmeetMet

Join our virtual seminar! @sedonamurphy.bsky.social presents cutting-edge research on 3D genome organisation & epigenetic memory in development, moderated by @stefanschoenfelder.bsky.social 📅 Jan 8, 4pm UK 💻 Zoom Register: us02web.zoom.us/webinar/regi... #3DGenome #Epigenetics #ChromatinBiology

Happy to share our new review on 3D chromatin organisation by cohesin with you. It was a great pleasure to review recent advances and future prospects with @danielgerlich.bsky.social.

Nature Reviews Molecular Cell Biology@natrevmcb.nature.com · 7mo ago

New Online! Organization of replicated chromosomes by DNA loops and sister chromatid cohesion

We are looking for a Postdoc at the Center for Gene Expression in Copenhagen. Deadline for applications is the 11th of January. If you are interested in 3D chromatin, SMC complexes, and super-resolution microscopy, join us. www.nature.com/naturecareer...

Postdocs at Center for Gene Expression in Department of Cellular and Molecular Medicine - Copenhagen, Hovedstaden (DK) job with University of Copenhagen | 12849488

We are looking for 2 or more highly motivated postdocs interested in ribosome biology, 3D chromatin organisation, or regulation of protein turnove...

nature.com

An ultra-rapid 3D immunostaining protocol can uniformly label organ-scale tissues go.nature.com/40wig8l rdcu.be/eUK9R

Uniform volumetric single-cell processing for organ-scale molecular phenotyping - Nature Biotechnology

An ultra-rapid 3D immunostaining protocol can uniformly label organ-scale tissues.

go.nature.com

Exciting new paper out! @allanaschooley.bsky.social and Sergey Venev led this project that let to the discovery of two chromosome folding programs: one inherited via mitotic chromosomes and one mitotic inherited through the cytoplasm! www.nature.com/articles/s41...

Interphase chromosome conformation is specified by distinct folding programmes inherited through mitotic chromosomes or the cytoplasm - Nature Cell Biology

Schooley et al. find that mitotically bookmarked loci drive a transient chromosome folding state during G1 entry that is subsequently modulated by factors inherited through the cytoplasm.

nature.com

🧬 Are you interested in synthetic biology, CRISPR-Cas9 genome editing and cutting-edge genomics? Apply by 07.01.2026 to join Stefan Mundlos’ lab @stemundi.bsky.social at the MPIMG. #IMPRS-BAC #gradschool! @nataliabenetti.bsky.social 👉 www.molgen.mpg.de/5124667/Mund...

Nuclear speckle associated RRM-containing proteins are block copolymers. They make size-limited, ordered microphases, tens of nm in size comprising tens of molecules. Speckles are likely clusters or emulsions of distinct microphases and not macrophases www.sciencedirect.com/science/arti...

Nuclear speckle proteins form intrinsic and MALAT1-dependent microphases

Pre-mRNA processing components in nuclear speckles encompass one or more folded RNA recognition motifs (RRMs) and disordered regions with specific seq…

sciencedirect.com

Very happy to share the published version of our study on the benefits of sodium sulfite + trolox (SST) as oxygen scavenger for #DNA-PAINT - now out in Small! Thanks to the reviewers for helpful comments and again congrats, Becky, on your PhD's first paper!! tinyurl.com/54m2pt9c

A Simple, Ultrastable, and Cost‐Effective Oxygen‐Scavenging System for Long‐Term DNA‐PAINT Imaging

A simple, enzyme-free, and cost-effective oxygen scavenging system enhances DNA-PAINT super-resolution microscopy by increasing photostability, minimizing docking strand degradation, and enabling fas...

onlinelibrary.wiley.com

Johannes Stein@jmstein.bsky.social · last yr.

(1/n) A simple, ultrastable, and cost-effective oxygen-scavenging system for long-term DNA-PAINT imaging Please check out our new study on the benefits of sodium sulfite as oxygen scavenging system for DNA-PAINT. 👇🧵 #SuperResolution #DNAPAINT #SMLM #Microscopy

Organelles do NOT have a single uniform pH. And if you think they must, because “protons diffuse fast,” this paper is for you. A thread on why that assumption is wrong; and what we found instead. 🧵 1/n

bioRxivpreprint@biorxivpreprint.bsky.social · 8mo ago

Organelles harbour pH gradients https://www.biorxiv.org/content/10.64898/2025.12.12.694065v1